LAMMPS (10 Feb 2021)
# kim property example
#
# For detailed information of this example please refer to:
# `https://openkim.org/doc/evaluation/tutorial-lammps/`
#
# Description:
#
# This example is designed to calculate the cohesive energy corresponding to
# the equilibrium FCC lattice constant for
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004` model for
# argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and
# `https://docs.lammps.org/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command.
#
# Requirement:
#
# This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://docs.lammps.org/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the
# `https://docs.lammps.org/Build_extras.html#kim` doc page for
# further details.
#
# This example requires that the KIM Portable Model (PM)
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004`
# is installed.  This can be done with the command
#   kim-api-collections-management install user LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
#   source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
#   source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
#

# Initialize interatomic potential (KIM model) and units
atom_style atomic

# Set the OpenKIM model that will be used
kim init LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 metal
#=== BEGIN kim init ==========================================
units metal
neighbor 2.0 bin   # Angstroms
timestep 1.0e-3    # picoseconds

This model has 3 mutable parameters. 
 No.      | Parameter name     | data type  | extent
-----------------------------------------------------
 1        | cutoff             | "Double"   | 1
 2        | epsilon            | "Double"   | 1
 3        | sigma              | "Double"   | 1
#=== END kim init ============================================


# the equilibrium lattice constant for the fcc structure
variable lattice_constant equal 5.248509056866169

# Periodic boundary conditions along all three dimensions
boundary p p p

# Create an FCC lattice with the lattice spacing
# using a single conventional (orthogonal) unit cell
lattice      fcc ${lattice_constant}
lattice      fcc 5.24850905686617
Lattice spacing in x,y,z = 5.2485091 5.2485091 5.2485091
region box   block 0 1 0 1 0 1 units lattice
create_box   1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.2485091 5.2485091 5.2485091)
  1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4 atoms
  create_atoms CPU = 0.000 seconds
mass         1 39.948

# Specify the KIM interactions
kim interactions Ar
#=== BEGIN kim interactions ==================================
pair_style kim LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004
pair_coeff * * Ar
#=== END kim interactions ====================================


# Compute energy
run 0

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Your simulation uses code contributions which should be cited:

- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6

@Article{tadmor:elliott:2011,
 author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
 title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
 journal = {{JOM}},
 year =    2011,
 volume =  63,
 number =  17,
 pages =   {17},
 doi =     {10.1007/s11837-011-0102-6}
}

- OpenKIM potential: https://openkim.org/cite/MO_126566794224_004#item-citation

@Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_126566794224_004a} is archived in OpenKIM~\cite{MO_126566794224_004, MD_498634107543_004, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_126566794224_004.bib}
\end{document}
}

@Misc{MO_126566794224_004,
  author       = {Ellad Tadmor},
  title        = {{L}ennard-{J}ones model (shifted) for {A}r with parameters from {B}ernardes (1958) (medium precision cutoff) v004},
  doi          = {10.25950/9f98b989},
  howpublished = {OpenKIM, \url{https://doi.org/10.25950/9f98b989}},
  keywords     = {OpenKIM, Model, MO_126566794224_004},
  publisher    = {OpenKIM},
  year         = 2020,
}

@Misc{MD_498634107543_004,
  author       = {Ellad Tadmor},
  title        = {{D}river for the {L}ennard-{J}ones model uniformly shifted to have zero energy at the cutoff radius v004},
  doi          = {10.25950/bdffd6a6},
  howpublished = {OpenKIM, \url{https://doi.org/10.25950/9f98b989}},
  keywords     = {OpenKIM, Model Driver, MD_498634107543_004},
  publisher    = {OpenKIM},
  year         = 2020,
}

@Article{tadmor:elliott:2011,
  author    = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
  title     = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
  journal   = {{JOM}},
  year      = {2011},
  volume    = {63},
  number    = {7},
  pages     = {17},
  doi       = {10.1007/s11837-011-0102-6},
}

@Misc{elliott:tadmor:2011,
  author       = {Ryan S. Elliott and Ellad B. Tadmor},
  title        = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
  howpublished = {\url{https://openkim.org/kim-api}},
  publisher    = {OpenKIM},
  year         = 2011,
  doi          = {10.25950/ff8f563a},
}

@Article{MO_126566794224_004a,
  author = {Newton Bernardes},
  doi = {10.1103/PhysRev.112.1534},
  issue = {5},
  journal = {Physical Review},
  pages = {1534--1539},
  publisher = {American Physical Society},
  title = {Theory of Solid {N}e, {A}, {K}r, and {X}e at 0{K}},
  volume = {112},
  year = {1958},
}
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Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 15.5
  ghost atom cutoff = 15.5
  binsize = 7.75, bins = 1 1 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 15.5
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.119 | 3.119 | 3.119 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0  -0.34602203            0  -0.34602203 0.00061471244 
Loop time of 3e-05 on 1 procs for 0 steps with 4 atoms

3.3% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0          | 0          | 0          |   0.0 |  0.00
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 3e-05      |            |       |100.00

Nlocal:        4.00000 ave           4 max           4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        1094.00 ave        1094 max        1094 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         0.00000 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:      1712.00 ave        1712 max        1712 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1712
Ave neighs/atom = 428.00000
Neighbor list builds = 0
Dangerous builds = 0

# Get cohesive energy
variable natoms       equal "count(all)"
variable ecohesive    equal "-pe/v_natoms"

# Create a property instance
kim property create 1 cohesive-potential-energy-cubic-crystal
#=== kim property ===========================================

# Set all the key-value pairs for this property instance
kim property modify 1 key short-name source-value 1 fcc                                                key species source-value 1 Ar                                                    key a source-value ${lattice_constant}                                                 source-unit angstrom                                                       key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0                                                   source-value 2 1:3 0.0 0.5 0.5                                                   source-value 3 1:3 0.5 0.0 0.5                                                   source-value 4 1:3 0.5 0.5 0.0                        key space-group source-value Fm-3m                                               key cohesive-potential-energy source-value ${ecohesive}                                                        source-unit eV
kim property modify 1 key short-name source-value 1 fcc                                                key species source-value 1 Ar                                                    key a source-value 5.24850905686617                                                 source-unit angstrom                                                       key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0                                                   source-value 2 1:3 0.0 0.5 0.5                                                   source-value 3 1:3 0.5 0.0 0.5                                                   source-value 4 1:3 0.5 0.5 0.0                        key space-group source-value Fm-3m                                               key cohesive-potential-energy source-value ${ecohesive}                                                        source-unit eV
kim property modify 1 key short-name source-value 1 fcc                                                key species source-value 1 Ar                                                    key a source-value 5.24850905686617                                                 source-unit angstrom                                                       key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0                                                   source-value 2 1:3 0.0 0.5 0.5                                                   source-value 3 1:3 0.5 0.0 0.5                                                   source-value 4 1:3 0.5 0.5 0.0                        key space-group source-value Fm-3m                                               key cohesive-potential-energy source-value 0.0865055084950546                                                        source-unit eV
#=== kim property ===========================================

# Dump the results in a file
kim property dump "results.edn"
#=== kim property ===========================================
Total wall time: 0:00:00
